PDBsum entry 2vbs

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Transferase PDB id
Protein chain
132 a.a. *
_CL ×2
Waters ×14
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Riboflavin kinase mj0056 from methanocaldococcus jannaschii in complex with po4
Structure: Riboflavin kinase. Chain: a. Synonym: protein mj0056. Engineered: yes
Source: Methanococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562
3.00Å     R-factor:   0.232     R-free:   0.282
Authors: M.D.Hartmann,S.Djuranovic,M.Ammelburg,J.Martin,A.N.Lupas, K.Zeth
Key ref:
M.Ammelburg et al. (2007). A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels. Structure, 15, 1577-1590. PubMed id: 18073108 DOI: 10.1016/j.str.2007.09.027
16-Sep-07     Release date:   20-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q60365  (RIFK_METJA) -  Riboflavin kinase
132 a.a.
132 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - CTP-dependent riboflavin kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: CTP + riboflavin = CDP + FMN
+ riboflavin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   3 terms 
  Biochemical function     nucleotide binding     7 terms  


DOI no: 10.1016/j.str.2007.09.027 Structure 15:1577-1590 (2007)
PubMed id: 18073108  
A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels.
M.Ammelburg, M.D.Hartmann, S.Djuranovic, V.Alva, K.K.Koretke, J.Martin, G.Sauer, V.Truffault, K.Zeth, A.N.Lupas, M.Coles.
Proteins of the cradle-loop barrel metafold are formed by duplication of a conserved betaalphabeta-element, suggesting a common evolutionary origin from an ancestral group of nucleic acid-binding proteins. The basal fold within this metafold, the RIFT barrel, is also found in a wide range of enzymes, whose homologous relationship with the nucleic acid-binding group is unclear. We have characterized a protein family that is intermediate in sequence and structure between the basal group of cradle-loop barrels and one family of RIFT-barrel enzymes, the riboflavin kinases. We report the structure, substrate-binding mode, and catalytic activity for one of these proteins, Methanocaldococcus jannaschii Mj0056, which is an archaeal riboflavin kinase. Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases.
  Selected figure(s)  
Figure 2.
Figure 2. Cluster Map of Mj0065 Homologs
The map, obtained with CLANS (see Experimental Procedures), shows Mj0056 in the context of double-psi barrels (AAA N domains, double-psi barrel enzymes), swapped-hairpin barrels (AbrB superfamily), and RIFT barrels (PhS018 group, riboflavin kinases, riboflavin synthases).
Figure 8.
Figure 8. Structural Comparison of Archaeal and Bacterial/Eukaryotic RFKs
Mj0056-MgCDP-FMN (A) is compared to HsRFK-MgADP-FMN (1Q9S) (B). A superposition of the nucleotide binding sites (C) illustrates how the absence of α1′ in HsRFK accommodates the larger adenosine moiety. The superimposition in (D) shows the FMN binding site, highlighting the structural equivalence of α1 in Mj0056 to the C-terminal extension in HsRFK.
  The above figures are reprinted by permission from Cell Press: Structure (2007, 15, 1577-1590) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19420061 S.Shi, B.Chitturi, and N.V.Grishin (2009).
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
  Nucleic Acids Res, 37, W526-W531.  
19609930 V.Alva, S.Dunin-Horkawicz, M.Habeck, M.Coles, and A.N.Lupas (2009).
The GD box: a widespread noncontiguous supersecondary structural element.
  Protein Sci, 18, 1961-1966.  
19558965 V.Y.Yatsyshyn, O.P.Ishchuk, A.Y.Voronovsky, D.V.Fedorovych, and A.A.Sibirny (2009).
Production of flavin mononucleotide by metabolically engineered yeast Candida famata.
  Metab Eng, 11, 163-167.  
18457946 V.Alva, K.K.Koretke, M.Coles, and A.N.Lupas (2008).
Cradle-loop barrels and the concept of metafolds in protein classification by natural descent.
  Curr Opin Struct Biol, 18, 358-365.  
18245297 Z.Mashhadi, H.Zhang, H.Xu, and R.H.White (2008).
Identification and characterization of an archaeon-specific riboflavin kinase.
  J Bacteriol, 190, 2615-2618.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.